Instead of cost-plus fixed-fee, it seems to me most of the government-funded R&D is in a matching funds format, especially for technology with commercial potential such as fuel cells or cancer treatment. (I work on a cost-plus contract but it is for something very specific that has absolutely no commercial value.)
For a typical matching funds example, Congress offers $7mil to a company willing to fund the remaining $15mil to develop a technology, find a cure, etc. This shuts out the little guy with a creative idea, in favor of an established powerhouse who will win the contract on current position in the industry, and just throw brute force (large-scale, old-paradigm technology) at the problem. Such an approach is problematic because it impedes the process of allowing new paradigms to emerge, which are often introduced by people regarded by the affected industry as outsiders.
Politics enable this stagnation. For example, the USDA is considering restructuring the carb-heavy food pyramid in light of recent revelations about low-carb diets. As you can imagine, every established high-carb interest is very active in getting their commodity (potatoes, milk, etc.) somehow built into the new food pyramid. The focus is on supporting the existing food paradigm, not improving dietary health information. Politics is bad for innovation, even in the pork belly guise of government-funded research, and unfortunately the US is pretty well bogged-down with special-interest politics.
Government funding aside, western concepts of intellectual property and fair use also provide obstacles to innovation in the free market. In the Asian economy there is less focus on or enforcement of copyright. As mentioned above, reverse-engineering was an accepted practice for years in Asia, and now they are just discovering better ways of doing the things we've been doing the same way for too long. Corporations there can readily fund their own R&D, without being sucked dry or torn down by armies of friendly and hostile patent attorneys.